From 8a8d3a566a4851ba7692a3e6f5790543997da8d8 Mon Sep 17 00:00:00 2001
From: Haibao Tang <htang@humanlongevity.com>
Date: Thu, 5 Jul 2018 19:29:17 -0700
Subject: [PATCH] [extract] Add bam flags

---
 extract.go | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/extract.go b/extract.go
index 5143f59..f650c52 100644
--- a/extract.go
+++ b/extract.go
@@ -589,8 +589,21 @@ func (r *Extracter) ExtractInterContigLinks() {
 			}
 			break
 		}
+		// Filtering: Unmapped | Secondary | QCFail | Duplicate | Supplementary
+		if rec.MapQ == 0 || rec.Flags&3844 != 0 {
+			continue
+		}
+
+		// Make sure we have these contig ids
 		at, bt := rec.Ref.Name(), rec.MateRef.Name()
-		ai, bi := r.contigToIdx[at], r.contigToIdx[bt]
+		ai, ok := r.contigToIdx[at]
+		if !ok {
+			continue
+		}
+		bi, ok := r.contigToIdx[bt]
+		if !ok {
+			continue
+		}
 
 		//         read1                                               read2
 		//     ---a-- X|----- dist = a2 ----|         |--- dist = b ---|X ------ b2 ------